Rules-wise, there is no inherent benefit in choosing dual daggers over dual shortswords, apart from the usually negligible differences in monetary cost and weight and the thrown property you mentioned. However, an enchanted dagger is usually better than a mundane shortsword, so it is possible for a determined dagger user to keep up if they get magical weapons such as the Dagger of Venom (Dungeon Master's Guide, p161).
It is also noteworthy that the thrown property of the daggers can be a fairly significant benefit in the hands of a capable rogue. Thrown daggers are eligible to trigger sneak attacks - this can be done with other ranged weapons as well, but daggers are advantageous for the action economy. Switching between a dedicated ranged weapon and a pair of swords takes time, while wielding another dagger to replace a thrown one is a free action. Therefore we could characterize a bow as the optimal weapon for a rogue who intends to stay at range, the twin short swords for those who want to inflict damage in melee, and dual daggers or shortsword with dagger for those who want to deal damage in melee while keeping a ranged option for flexibility.
A little note regarding the above, though: the Player's Handbook is a bit vague on whether one actually has to wield a weapon before throwing it. Everyone I've played with has assumed that, since the thrown property lacks an explicit mention that drawing the projectile is a part of the action, one indeed has to separately wield the weapon (note that the ammunition property does state that drawing the projectile is a part of the action). Whichever way you interpret it is your choice, but be aware that allowing throwing daggers without wielding them will reduce the relative utility of daggers as melee weapons. If you follow the common ruling that thrown weapons have to be wielded first, the thrown property makes them worthwhile - make sure the player of the rogue is aware of this.
More open situations
Depending on your playstyle, the player may receive benefits from having highly concealable weapons. For example if the campaign is heavy on "social stealth" where the player characters are expected to blend into crowds without being obviously threatening, having daggers instead of swords can be a considerable boon to the point of making mundane daggers superior to shortswords. The actual difference depends heavily on the type of challenges encountered by the party and how the GM treats these challenges.
Bonus: brief comparison to rapier
As the rogue gains levels, their sneak attack will gradually become their dominant source of damage to the point of making the weapon's base damage die almost meaningless. Compared to the rapier option, dual short swords and dual daggers are indeed usually better, largely because they have a greater probability to hit than a single rapier blow and thus provide the rogue a greater chance to activate the sneak attack. A less known, and usually far less significant benefit the short swords and daggers is their ability to strike underwater without disadvantage (Player's Handbook, p198; basic rules).